Characterization and genetic analysis of an EIN4-like sequence (CaETR-1) located in QTLAR1 implicated in ascochyta blight resistance in chickpea

Abstract

Two alleles of a chickpea (Cicer arietinum L.) ethylene receptor-like sequence (CaETR-1) were sequence-characterized using synteny analysis with genome sequences of Medicago truncatula L. The full length of the sequence obtained in the accession FLIP84-92C resistant to ascochyta blight (CaETR-1a) span 4,428 bp, including the polyadenylation signal in the 3'-untranslated region (UTR), whereas it has a 730 bp deletion in the 3'-UTR region in the susceptible accession PI359075 (CaETR-1b). The deduced protein belongs to subfamily II of the ethylene receptors and contains all the domains that define EIN4 homologs in Arabidopsis. The EIN4-like sequence (CaETR-1) has been mapped using a recombinant inbred line (RIL) population derived from an intraspecific cross between ILC3279 and WR315, resistant and susceptible to blight, respectively. The locus was located in LGIVa of the genetic map, flanked by markers NCPGR91 and GAA47 (at distances of 11.3 and 17.9 cM, respectively). This is the first potentially functional sequence identified under a QTL peak for ascochyta blight resistance in chickpea (QTL(AR1)). This EIN4-like (CaETR-1) sequence explained up to 33.8% of the total phenotypic variation. This sequence could be directly related to blight resistance, together with other QTLs that have been found to be involved in resistance to this major chickpea disease.

Allele-specific amplification for the detection of ascochyta blight resistance in chickpea

“…2). To address this problem, a specific primer (CaETR-Rev2) for the resistance allele (Ca-ETR-1a) was designed based on the 3 0 UTR region that is absent in the susceptible allele (Madrid et al 2012) (Fig. 1).…”

“…Nevertheless, four resistant genotypes (ILC 482, 'Juano', 'Myles' and 'Krema') did not show any of these two resistance alleles. Considering the tight linkage between the markers and their respective QTLs (Madrid et al 2012;Iruela et al 2006), these genotypes may actually carry different genes or QTLs for resistance to ascochyta blight. For example, QTL AR3 on LG2 was reported to be tightly linked to a microsatellite marker (STMS TA194) (Iruela et al 2007).…”

“…Using the sequence information of the two alleles CaETR-1a (HQ009510) and CaETR-1b (HQ009511) described for a gene located at QTL AR1 (Madrid et al 2012) three primers (CaETR-Fw: 5 0 -CAGGAAGTT CAATGGCCCTA-3 0 ; CaETR-Rev1: 5 0 -TAAGTTGT GACAAAAGACTCAATCG-3 0 ; and CaETR-Rev2: 5 0 -TGTGGCACAGTGGACCCCATCT-3 0 ) were designed . For amplification, the thermocycler was programmed for 30 cycles with the following temperature profile: 95°C for 30 s, 60°C for 30 s and 72°C for 1 min followed by a final extension at 72°C for 7 min.…”

“…However, a homologue to the Arabidopsis thaliana ethylene insensitive 4 gene (EIN4) has recently been reported in chickpea (Madrid et al 2012) which mapped to QTL AR1 . Two different alleles (CaETR-1a, CaETR-1b) were shown to be associated with ascochyta blight resistance and susceptibility, respectively.…”

Achievements and Challenges in Legume Breeding for Pest and Disease Resistance

“…The identification of the homologous region of a QTL in the model legume M. truncatula through microsynteny is a good approach to identify candidate genes involved in the control of resistance, or at least molecular Downloaded by [West Virginia University] at 06:40 20 November 2014 markers more tightly linked with resistance, in species with less saturated maps. This approach has been used for example in resistance to ascochyta blight in chickpea (Madrid et al, 2012), for identifying in pea the SYM2 gene involved in symbiosis (Gualtieri et al, 2002) and in resistance to broomrape (Cobos et al, 2013).…”